apps/workbench/app/controllers/collections_controller.rb

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 require "arvados/keep"
   6 require "arvados/collection"
   7 require "uri"
   8
   9 class CollectionsController < ApplicationController
  10   include ActionController::Live
  11
  12   skip_around_filter :require_thread_api_token, if: proc { |ctrl|
  13     Rails.configuration.anonymous_user_token and
  14     'show' == ctrl.action_name
  15   }
  16   skip_around_filter(:require_thread_api_token,
  17                      only: [:show_file, :show_file_links])
  18   skip_before_filter(:find_object_by_uuid,
  19                      only: [:provenance, :show_file, :show_file_links])
  20   # We depend on show_file to display the user agreement:
  21   skip_before_filter :check_user_agreements, only: :show_file
  22   skip_before_filter :check_user_profile, only: :show_file
  23
  24   RELATION_LIMIT = 5
  25
  26   def show_pane_list
  27     panes = %w(Files Upload Tags Provenance_graph Used_by Advanced)
  28     panes = panes - %w(Upload) unless (@object.editable? rescue false)
  29     panes
  30   end
  31
  32   def set_persistent
  33     case params[:value]
  34     when 'persistent', 'cache'
  35       persist_links = Link.filter([['owner_uuid', '=', current_user.uuid],
  36                                    ['link_class', '=', 'resources'],
  37                                    ['name', '=', 'wants'],
  38                                    ['tail_uuid', '=', current_user.uuid],
  39                                    ['head_uuid', '=', @object.uuid]])
  40       logger.debug persist_links.inspect
  41     else
  42       return unprocessable "Invalid value #{value.inspect}"
  43     end
  44     if params[:value] == 'persistent'
  45       if not persist_links.any?
  46         Link.create(link_class: 'resources',
  47                     name: 'wants',
  48                     tail_uuid: current_user.uuid,
  49                     head_uuid: @object.uuid)
  50       end
  51     else
  52       persist_links.each do |link|
  53         link.destroy || raise
  54       end
  55     end
  56
  57     respond_to do |f|
  58       f.json { render json: @object }
  59     end
  60   end
  61
  62   def index
  63     # API server index doesn't return manifest_text by default, but our
  64     # callers want it unless otherwise specified.
  65     @select ||= Collection.columns.map(&:name)
  66     base_search = Collection.select(@select)
  67     if params[:search].andand.length.andand > 0
  68       tags = Link.where(any: ['contains', params[:search]])
  69       @objects = (base_search.where(uuid: tags.collect(&:head_uuid)) |
  70                       base_search.where(any: ['contains', params[:search]])).
  71         uniq { |c| c.uuid }
  72     else
  73       if params[:limit]
  74         limit = params[:limit].to_i
  75       else
  76         limit = 100
  77       end
  78
  79       if params[:offset]
  80         offset = params[:offset].to_i
  81       else
  82         offset = 0
  83       end
  84
  85       @objects = base_search.limit(limit).offset(offset)
  86     end
  87     @links = Link.where(head_uuid: @objects.collect(&:uuid))
  88     @collection_info = {}
  89     @objects.each do |c|
  90       @collection_info[c.uuid] = {
  91         tag_links: [],
  92         wanted: false,
  93         wanted_by_me: false,
  94         provenance: [],
  95         links: []
  96       }
  97     end
  98     @links.each do |link|
  99       @collection_info[link.head_uuid] ||= {}
 100       info = @collection_info[link.head_uuid]
 101       case link.link_class
 102       when 'tag'
 103         info[:tag_links] << link
 104       when 'resources'
 105         info[:wanted] = true
 106         info[:wanted_by_me] ||= link.tail_uuid == current_user.uuid
 107       when 'provenance'
 108         info[:provenance] << link.name
 109       end
 110       info[:links] << link
 111     end
 112     @request_url = request.url
 113
 114     render_index
 115   end
 116
 117   def show_file_links
 118     Thread.current[:reader_tokens] = [params[:reader_token]]
 119     return if false.equal?(find_object_by_uuid)
 120     render layout: false
 121   end
 122
 123   def show_file
 124     # We pipe from arv-get to send the file to the user.  Before we start it,
 125     # we ask the API server if the file actually exists.  This serves two
 126     # purposes: it lets us return a useful status code for common errors, and
 127     # helps us figure out which token to provide to arv-get.
 128     # The order of searched tokens is important: because the anonymous user
 129     # token is passed along with every API request, we have to check it first.
 130     # Otherwise, it's impossible to know whether any other request succeeded
 131     # because of the reader token.
 132     coll = nil
 133     tokens = [(Rails.configuration.anonymous_user_token || nil),
 134               params[:reader_token],
 135               Thread.current[:arvados_api_token]].compact
 136     usable_token = find_usable_token(tokens) do
 137       coll = Collection.find(params[:uuid])
 138     end
 139     if usable_token.nil?
 140       # Response already rendered.
 141       return
 142     end
 143
 144     # If we are configured to use a keep-web server, just redirect to
 145     # the appropriate URL.
 146     if Rails.configuration.keep_web_url or
 147         Rails.configuration.keep_web_download_url
 148       opts = {}
 149       if usable_token == params[:reader_token]
 150         opts[:path_token] = usable_token
 151       elsif usable_token == Rails.configuration.anonymous_user_token
 152         # Don't pass a token at all
 153       else
 154         # We pass the current user's real token only if it's necessary
 155         # to read the collection.
 156         opts[:query_token] = usable_token
 157       end
 158       opts[:disposition] = params[:disposition] if params[:disposition]
 159       return redirect_to keep_web_url(params[:uuid], params[:file], opts)
 160     end
 161
 162     # No keep-web server available. Get the file data with arv-get,
 163     # and serve it through Rails.
 164
 165     file_name = params[:file].andand.sub(/^(\.\/|\/|)/, './')
 166     if file_name.nil? or not coll.manifest.has_file?(file_name)
 167       return render_not_found
 168     end
 169
 170     opts = params.merge(arvados_api_token: usable_token)
 171
 172     # Handle Range requests. Currently we support only 'bytes=0-....'
 173     if request.headers.include? 'HTTP_RANGE'
 174       if m = /^bytes=0-(\d+)/.match(request.headers['HTTP_RANGE'])
 175         opts[:maxbytes] = m[1]
 176         size = params[:size] || '*'
 177         self.response.status = 206
 178         self.response.headers['Content-Range'] = "bytes 0-#{m[1]}/#{size}"
 179       end
 180     end
 181
 182     ext = File.extname(params[:file])
 183     self.response.headers['Content-Type'] =
 184       Rack::Mime::MIME_TYPES[ext] || 'application/octet-stream'
 185     if params[:size]
 186       size = params[:size].to_i
 187       if opts[:maxbytes]
 188         size = [size, opts[:maxbytes].to_i].min
 189       end
 190       self.response.headers['Content-Length'] = size.to_s
 191     end
 192     self.response.headers['Content-Disposition'] = params[:disposition] if params[:disposition]
 193     begin
 194       file_enumerator(opts).each do |bytes|
 195         response.stream.write bytes
 196       end
 197     ensure
 198       response.stream.close
 199     end
 200   end
 201
 202   def sharing_scopes
 203     ["GET /arvados/v1/collections/#{@object.uuid}", "GET /arvados/v1/collections/#{@object.uuid}/", "GET /arvados/v1/keep_services/accessible"]
 204   end
 205
 206   def search_scopes
 207     begin
 208       ApiClientAuthorization.filter([['scopes', '=', sharing_scopes]]).results
 209     rescue ArvadosApiClient::AccessForbiddenException
 210       nil
 211     end
 212   end
 213
 214   def find_object_by_uuid
 215     if not Keep::Locator.parse params[:id]
 216       super
 217     end
 218   end
 219
 220   def show
 221     return super if !@object
 222
 223     @logs = []
 224
 225     if params["tab_pane"] == "Provenance_graph"
 226       @prov_svg = ProvenanceHelper::create_provenance_graph(@object.provenance, "provenance_svg",
 227                                                             {:request => request,
 228                                                              :direction => :top_down,
 229                                                              :combine_jobs => :script_only}) rescue nil
 230     end
 231
 232     if current_user
 233       if Keep::Locator.parse params["uuid"]
 234         @same_pdh = Collection.filter([["portable_data_hash", "=", @object.portable_data_hash]]).limit(20)
 235         if @same_pdh.results.size == 1
 236           redirect_to collection_path(@same_pdh[0]["uuid"])
 237           return
 238         end
 239         owners = @same_pdh.map(&:owner_uuid).to_a.uniq
 240         preload_objects_for_dataclass Group, owners
 241         preload_objects_for_dataclass User, owners
 242         uuids = @same_pdh.map(&:uuid).to_a.uniq
 243         preload_links_for_objects uuids
 244         render 'hash_matches'
 245         return
 246       else
 247         if Job.api_exists?(:index)
 248           jobs_with = lambda do |conds|
 249             Job.limit(RELATION_LIMIT).where(conds)
 250               .results.sort_by { |j| j.finished_at || j.created_at }
 251           end
 252           @output_of = jobs_with.call(output: @object.portable_data_hash)
 253           @log_of = jobs_with.call(log: @object.portable_data_hash)
 254         end
 255
 256         @project_links = Link.limit(RELATION_LIMIT).order("modified_at DESC")
 257           .where(head_uuid: @object.uuid, link_class: 'name').results
 258         project_hash = Group.where(uuid: @project_links.map(&:tail_uuid)).to_hash
 259         @projects = project_hash.values
 260
 261         @permissions = Link.limit(RELATION_LIMIT).order("modified_at DESC")
 262           .where(head_uuid: @object.uuid, link_class: 'permission',
 263                  name: 'can_read').results
 264         @search_sharing = search_scopes
 265
 266         if params["tab_pane"] == "Used_by"
 267           @used_by_svg = ProvenanceHelper::create_provenance_graph(@object.used_by, "used_by_svg",
 268                                                                    {:request => request,
 269                                                                     :direction => :top_down,
 270                                                                     :combine_jobs => :script_only,
 271                                                                     :pdata_only => true}) rescue nil
 272         end
 273       end
 274     end
 275     super
 276   end
 277
 278   def sharing_popup
 279     @search_sharing = search_scopes
 280     render("sharing_popup.js", content_type: "text/javascript")
 281   end
 282
 283   helper_method :download_link
 284
 285   def download_link
 286     collections_url + "/download/#{@object.uuid}/#{@search_sharing.first.api_token}/"
 287   end
 288
 289   def share
 290     ApiClientAuthorization.create(scopes: sharing_scopes)
 291     sharing_popup
 292   end
 293
 294   def unshare
 295     search_scopes.each do |s|
 296       s.destroy
 297     end
 298     sharing_popup
 299   end
 300
 301   def remove_selected_files
 302     uuids, source_paths = selected_collection_files params
 303
 304     arv_coll = Arv::Collection.new(@object.manifest_text)
 305     source_paths[uuids[0]].each do |p|
 306       arv_coll.rm "."+p
 307     end
 308
 309     if @object.update_attributes manifest_text: arv_coll.manifest_text
 310       show
 311     else
 312       self.render_error status: 422
 313     end
 314   end
 315
 316   def update
 317     updated_attr = params[:collection].each.select {|a| a[0].andand.start_with? 'rename-file-path:'}
 318
 319     if updated_attr.size > 0
 320       # Is it file rename?
 321       file_path = updated_attr[0][0].split('rename-file-path:')[-1]
 322
 323       new_file_path = updated_attr[0][1]
 324       if new_file_path.start_with?('./')
 325         # looks good
 326       elsif new_file_path.start_with?('/')
 327         new_file_path = '.' + new_file_path
 328       else
 329         new_file_path = './' + new_file_path
 330       end
 331
 332       arv_coll = Arv::Collection.new(@object.manifest_text)
 333
 334       if arv_coll.exist?(new_file_path)
 335         @errors = 'Duplicate file path. Please use a different name.'
 336         self.render_error status: 422
 337       else
 338         arv_coll.rename "./"+file_path, new_file_path
 339
 340         if @object.update_attributes manifest_text: arv_coll.manifest_text
 341           show
 342         else
 343           self.render_error status: 422
 344         end
 345       end
 346     else
 347       # Not a file rename; use default
 348       super
 349     end
 350   end
 351
 352   def tags
 353     render
 354   end
 355
 356   def save_tags
 357     tags_param = params['tag_data']
 358     if tags_param
 359       if tags_param.is_a?(String) && tags_param == "empty"
 360         tags = {}
 361       else
 362         tags = tags_param
 363       end
 364     end
 365
 366     if tags
 367       if @object.update_attributes properties: tags
 368         @saved_tags = true
 369         render
 370       else
 371         self.render_error status: 422
 372       end
 373     end
 374   end
 375
 376   protected
 377
 378   def find_usable_token(token_list)
 379     # Iterate over every given token to make it the current token and
 380     # yield the given block.
 381     # If the block succeeds, return the token it used.
 382     # Otherwise, render an error response based on the most specific
 383     # error we encounter, and return nil.
 384     most_specific_error = [401]
 385     token_list.each do |api_token|
 386       begin
 387         # We can't load the corresponding user, because the token may not
 388         # be scoped for that.
 389         using_specific_api_token(api_token, load_user: false) do
 390           yield
 391           return api_token
 392         end
 393       rescue ArvadosApiClient::ApiError => error
 394         if error.api_status >= most_specific_error.first
 395           most_specific_error = [error.api_status, error]
 396         end
 397       end
 398     end
 399     case most_specific_error.shift
 400     when 401, 403
 401       redirect_to_login
 402     when 404
 403       render_not_found(*most_specific_error)
 404     end
 405     return nil
 406   end
 407
 408   def keep_web_url(uuid_or_pdh, file, opts)
 409     munged_id = uuid_or_pdh.sub('+', '-')
 410     fmt = {uuid_or_pdh: munged_id}
 411
 412     tmpl = Rails.configuration.keep_web_url
 413     if Rails.configuration.keep_web_download_url and
 414         (!tmpl or opts[:disposition] == 'attachment')
 415       # Prefer the attachment-only-host when we want an attachment
 416       # (and when there is no preview link configured)
 417       tmpl = Rails.configuration.keep_web_download_url
 418     elsif not Rails.configuration.trust_all_content
 419       check_uri = URI.parse(tmpl % fmt)
 420       if opts[:query_token] and
 421           not check_uri.host.start_with?(munged_id + "--") and
 422           not check_uri.host.start_with?(munged_id + ".")
 423         # We're about to pass a token in the query string, but
 424         # keep-web can't accept that safely at a single-origin URL
 425         # template (unless it's -attachment-only-host).
 426         tmpl = Rails.configuration.keep_web_download_url
 427         if not tmpl
 428           raise ArgumentError, "Download precluded by site configuration"
 429         end
 430         logger.warn("Using download link, even though inline content " \
 431                     "was requested: #{check_uri.to_s}")
 432       end
 433     end
 434
 435     if tmpl == Rails.configuration.keep_web_download_url
 436       # This takes us to keep-web's -attachment-only-host so there is
 437       # no need to add ?disposition=attachment.
 438       opts.delete :disposition
 439     end
 440
 441     uri = URI.parse(tmpl % fmt)
 442     uri.path += '/' unless uri.path.end_with? '/'
 443     if opts[:path_token]
 444       uri.path += 't=' + opts[:path_token] + '/'
 445     end
 446     uri.path += '_/'
 447     uri.path += URI.escape(file)
 448
 449     query = Hash[URI.decode_www_form(uri.query || '')]
 450     { query_token: 'api_token',
 451       disposition: 'disposition' }.each do |opt, param|
 452       if opts.include? opt
 453         query[param] = opts[opt]
 454       end
 455     end
 456     unless query.empty?
 457       uri.query = URI.encode_www_form(query)
 458     end
 459
 460     uri.to_s
 461   end
 462
 463   # Note: several controller and integration tests rely on stubbing
 464   # file_enumerator to return fake file content.
 465   def file_enumerator opts
 466     FileStreamer.new opts
 467   end
 468
 469   class FileStreamer
 470     include ArvadosApiClientHelper
 471     def initialize(opts={})
 472       @opts = opts
 473     end
 474     def each
 475       return unless @opts[:uuid] && @opts[:file]
 476
 477       env = Hash[ENV].dup
 478
 479       require 'uri'
 480       u = URI.parse(arvados_api_client.arvados_v1_base)
 481       env['ARVADOS_API_HOST'] = "#{u.host}:#{u.port}"
 482       env['ARVADOS_API_TOKEN'] = @opts[:arvados_api_token]
 483       env['ARVADOS_API_HOST_INSECURE'] = "true" if Rails.configuration.arvados_insecure_https
 484
 485       bytesleft = @opts[:maxbytes].andand.to_i || 2**16
 486       io = IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"], 'rb')
 487       while bytesleft > 0 && (buf = io.read([bytesleft, 2**16].min)) != nil
 488         # shrink the bytesleft count, if we were given a maximum byte
 489         # count to read
 490         if @opts.include? :maxbytes
 491           bytesleft = bytesleft - buf.length
 492         end
 493         yield buf
 494       end
 495       io.close
 496       # "If ios is opened by IO.popen, close sets $?."
 497       # http://www.ruby-doc.org/core-2.1.3/IO.html#method-i-close
 498       Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
 499     end
 500   end
 501 end