apps/workbench/app/controllers/collections_controller.rb

   1 class CollectionsController < ApplicationController
   2   skip_around_filter(:thread_with_mandatory_api_token,
   3                      only: [:show_file, :show_file_links])
   4   skip_before_filter(:find_object_by_uuid,
   5                      only: [:provenance, :show_file, :show_file_links])
   6
   7   RELATION_LIMIT = 5
   8
   9   def show_pane_list
  10     %w(Files Provenance_graph Used_by Advanced)
  11   end
  12
  13   def set_persistent
  14     case params[:value]
  15     when 'persistent', 'cache'
  16       persist_links = Link.filter([['owner_uuid', '=', current_user.uuid],
  17                                    ['link_class', '=', 'resources'],
  18                                    ['name', '=', 'wants'],
  19                                    ['tail_uuid', '=', current_user.uuid],
  20                                    ['head_uuid', '=', @object.uuid]])
  21       logger.debug persist_links.inspect
  22     else
  23       return unprocessable "Invalid value #{value.inspect}"
  24     end
  25     if params[:value] == 'persistent'
  26       if not persist_links.any?
  27         Link.create(link_class: 'resources',
  28                     name: 'wants',
  29                     tail_uuid: current_user.uuid,
  30                     head_uuid: @object.uuid)
  31       end
  32     else
  33       persist_links.each do |link|
  34         link.destroy || raise
  35       end
  36     end
  37
  38     respond_to do |f|
  39       f.json { render json: @object }
  40     end
  41   end
  42
  43   def choose
  44     params[:limit] ||= 20
  45     @objects = Link.
  46       filter([['link_class','=','name'],
  47               ['head_uuid','is_a','arvados#collection']])
  48     find_objects_for_index
  49     @next_page_href = (next_page_offset and
  50                        url_for(offset: next_page_offset, partial: true))
  51     @name_links = @objects
  52     @objects = Collection.
  53       filter([['uuid','in',@name_links.collect(&:head_uuid)]])
  54     super
  55   end
  56
  57   def index
  58     if params[:search].andand.length.andand > 0
  59       tags = Link.where(any: ['contains', params[:search]])
  60       @collections = (Collection.where(uuid: tags.collect(&:head_uuid)) |
  61                       Collection.where(any: ['contains', params[:search]])).
  62         uniq { |c| c.uuid }
  63     else
  64       if params[:limit]
  65         limit = params[:limit].to_i
  66       else
  67         limit = 100
  68       end
  69
  70       if params[:offset]
  71         offset = params[:offset].to_i
  72       else
  73         offset = 0
  74       end
  75
  76       @collections = Collection.limit(limit).offset(offset)
  77     end
  78     @links = Link.limit(1000).
  79       where(head_uuid: @collections.collect(&:uuid))
  80     @collection_info = {}
  81     @collections.each do |c|
  82       @collection_info[c.uuid] = {
  83         tag_links: [],
  84         wanted: false,
  85         wanted_by_me: false,
  86         provenance: [],
  87         links: []
  88       }
  89     end
  90     @links.each do |link|
  91       @collection_info[link.head_uuid] ||= {}
  92       info = @collection_info[link.head_uuid]
  93       case link.link_class
  94       when 'tag'
  95         info[:tag_links] << link
  96       when 'resources'
  97         info[:wanted] = true
  98         info[:wanted_by_me] ||= link.tail_uuid == current_user.uuid
  99       when 'provenance'
 100         info[:provenance] << link.name
 101       end
 102       info[:links] << link
 103     end
 104     @request_url = request.url
 105   end
 106
 107   def show_file_links
 108     Thread.current[:reader_tokens] = [params[:reader_token]]
 109     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     if usable_token.nil?
 124       return  # Response already rendered.
 125     elsif params[:file].nil? or not file_in_collection?(coll, params[:file])
 126       return render_not_found
 127     end
 128     opts = params.merge(arvados_api_token: usable_token)
 129     ext = File.extname(params[:file])
 130     self.response.headers['Content-Type'] =
 131       Rack::Mime::MIME_TYPES[ext] || 'application/octet-stream'
 132     self.response.headers['Content-Length'] = params[:size] if params[:size]
 133     self.response.headers['Content-Disposition'] = params[:disposition] if params[:disposition]
 134     self.response_body = file_enumerator opts
 135   end
 136
 137   def sharing_scopes
 138     ["GET /arvados/v1/collections/#{@object.uuid}", "GET /arvados/v1/collections/#{@object.uuid}/", "GET /arvados/v1/keep_services/accessible"]
 139   end
 140
 141   def search_scopes
 142     begin
 143       ApiClientAuthorization.filter([['scopes', '=', sharing_scopes]]).results
 144     rescue ArvadosApiClient::AccessForbiddenException
 145       nil
 146     end
 147   end
 148
 149   def show
 150     return super if !@object
 151     if current_user
 152       jobs_with = lambda do |conds|
 153         Job.limit(RELATION_LIMIT).where(conds)
 154           .results.sort_by { |j| j.finished_at || j.created_at }
 155       end
 156       @output_of = jobs_with.call(output: @object.uuid)
 157       @log_of = jobs_with.call(log: @object.uuid)
 158       folder_links = Link.limit(RELATION_LIMIT).order("modified_at DESC")
 159         .where(head_uuid: @object.uuid, link_class: 'name').results
 160       folder_hash = Group.where(uuid: folder_links.map(&:tail_uuid)).to_hash
 161       @folders = folder_links.map { |link| folder_hash[link.tail_uuid] }
 162       @permissions = Link.limit(RELATION_LIMIT).order("modified_at DESC")
 163         .where(head_uuid: @object.uuid, link_class: 'permission',
 164                name: 'can_read').results
 165       @logs = Log.limit(RELATION_LIMIT).order("created_at DESC")
 166         .where(object_uuid: @object.uuid).results
 167       @is_persistent = Link.limit(1)
 168         .where(head_uuid: @object.uuid, tail_uuid: current_user.uuid,
 169                link_class: 'resources', name: 'wants')
 170         .results.any?
 171       @search_sharing = search_scopes
 172     end
 173     @prov_svg = ProvenanceHelper::create_provenance_graph(@object.provenance, "provenance_svg",
 174                                                           {:request => request,
 175                                                             :direction => :bottom_up,
 176                                                             :combine_jobs => :script_only}) rescue nil
 177     @used_by_svg = ProvenanceHelper::create_provenance_graph(@object.used_by, "used_by_svg",
 178                                                              {:request => request,
 179                                                                :direction => :top_down,
 180                                                                :combine_jobs => :script_only,
 181                                                                :pdata_only => true}) rescue nil
 182   end
 183
 184   def sharing_popup
 185     @search_sharing = search_scopes
 186     respond_to do |format|
 187       format.html
 188       format.js
 189     end
 190   end
 191
 192   helper_method :download_link
 193
 194   def download_link
 195     collections_url + "/download/#{@object.uuid}/#{@search_sharing.first.api_token}"
 196   end
 197
 198   def share
 199     a = ApiClientAuthorization.create(scopes: sharing_scopes)
 200     @search_sharing = search_scopes
 201     render 'sharing_popup'
 202   end
 203
 204   def unshare
 205     @search_sharing = search_scopes
 206     @search_sharing.each do |s|
 207       s.destroy
 208     end
 209     @search_sharing = search_scopes
 210     render 'sharing_popup'
 211   end
 212
 213   protected
 214
 215   def find_usable_token(token_list)
 216     # Iterate over every given token to make it the current token and
 217     # yield the given block.
 218     # If the block succeeds, return the token it used.
 219     # Otherwise, render an error response based on the most specific
 220     # error we encounter, and return nil.
 221     most_specific_error = [401]
 222     token_list.each do |api_token|
 223       using_specific_api_token(api_token) do
 224         begin
 225           yield
 226           return api_token
 227         rescue ArvadosApiClient::NotLoggedInException => error
 228           status = 401
 229         rescue => error
 230           status = (error.message =~ /\[API: (\d+)\]$/) ? $1.to_i : nil
 231           raise unless [401, 403, 404].include?(status)
 232         end
 233         if status >= most_specific_error.first
 234           most_specific_error = [status, error]
 235         end
 236       end
 237     end
 238     case most_specific_error.shift
 239     when 401, 403
 240       redirect_to_login
 241     when 404
 242       render_not_found(*most_specific_error)
 243     end
 244     return nil
 245   end
 246
 247   def file_in_collection?(collection, filename)
 248     target = CollectionsHelper.file_path(File.split(filename))
 249     collection.files.each do |file_spec|
 250       return true if (CollectionsHelper.file_path(file_spec) == target)
 251     end
 252     false
 253   end
 254
 255   def file_enumerator(opts)
 256     FileStreamer.new opts
 257   end
 258
 259   class FileStreamer
 260     include ArvadosApiClientHelper
 261     def initialize(opts={})
 262       @opts = opts
 263     end
 264     def each
 265       return unless @opts[:uuid] && @opts[:file]
 266
 267       env = Hash[ENV].dup
 268
 269       require 'uri'
 270       u = URI.parse(arvados_api_client.arvados_v1_base)
 271       env['ARVADOS_API_HOST'] = "#{u.host}:#{u.port}"
 272       env['ARVADOS_API_TOKEN'] = @opts[:arvados_api_token]
 273       env['ARVADOS_API_HOST_INSECURE'] = "true" if Rails.configuration.arvados_insecure_https
 274
 275       IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"],
 276                'rb') do |io|
 277         while buf = io.read(2**16)
 278           yield buf
 279         end
 280       end
 281       Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
 282     end
 283   end
 284 end