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   # We depend on show_file to display the user agreement:
   7   skip_before_filter :check_user_agreements, only: [:show_file]
   8
   9   RELATION_LIMIT = 5
  10
  11   def show_pane_list
  12     %w(Files Provenance_graph Used_by Advanced)
  13   end
  14
  15   def set_persistent
  16     case params[:value]
  17     when 'persistent', 'cache'
  18       persist_links = Link.filter([['owner_uuid', '=', current_user.uuid],
  19                                    ['link_class', '=', 'resources'],
  20                                    ['name', '=', 'wants'],
  21                                    ['tail_uuid', '=', current_user.uuid],
  22                                    ['head_uuid', '=', @object.uuid]])
  23       logger.debug persist_links.inspect
  24     else
  25       return unprocessable "Invalid value #{value.inspect}"
  26     end
  27     if params[:value] == 'persistent'
  28       if not persist_links.any?
  29         Link.create(link_class: 'resources',
  30                     name: 'wants',
  31                     tail_uuid: current_user.uuid,
  32                     head_uuid: @object.uuid)
  33       end
  34     else
  35       persist_links.each do |link|
  36         link.destroy || raise
  37       end
  38     end
  39
  40     respond_to do |f|
  41       f.json { render json: @object }
  42     end
  43   end
  44
  45   def choose
  46     params[:limit] ||= 20
  47     @objects = Link.
  48       filter([['link_class','=','name'],
  49               ['head_uuid','is_a','arvados#collection']])
  50     find_objects_for_index
  51     @next_page_href = (next_page_offset and
  52                        url_for(offset: next_page_offset, partial: true))
  53     @name_links = @objects
  54     @objects = Collection.
  55       filter([['uuid','in',@name_links.collect(&:head_uuid)]])
  56     super
  57   end
  58
  59   def index
  60     if params[:search].andand.length.andand > 0
  61       tags = Link.where(any: ['contains', params[:search]])
  62       @collections = (Collection.where(uuid: tags.collect(&:head_uuid)) |
  63                       Collection.where(any: ['contains', params[:search]])).
  64         uniq { |c| c.uuid }
  65     else
  66       if params[:limit]
  67         limit = params[:limit].to_i
  68       else
  69         limit = 100
  70       end
  71
  72       if params[:offset]
  73         offset = params[:offset].to_i
  74       else
  75         offset = 0
  76       end
  77
  78       @collections = Collection.limit(limit).offset(offset)
  79     end
  80     @links = Link.limit(1000).
  81       where(head_uuid: @collections.collect(&:uuid))
  82     @collection_info = {}
  83     @collections.each do |c|
  84       @collection_info[c.uuid] = {
  85         tag_links: [],
  86         wanted: false,
  87         wanted_by_me: false,
  88         provenance: [],
  89         links: []
  90       }
  91     end
  92     @links.each do |link|
  93       @collection_info[link.head_uuid] ||= {}
  94       info = @collection_info[link.head_uuid]
  95       case link.link_class
  96       when 'tag'
  97         info[:tag_links] << link
  98       when 'resources'
  99         info[:wanted] = true
 100         info[:wanted_by_me] ||= link.tail_uuid == current_user.uuid
 101       when 'provenance'
 102         info[:provenance] << link.name
 103       end
 104       info[:links] << link
 105     end
 106     @request_url = request.url
 107   end
 108
 109   def show_file_links
 110     Thread.current[:reader_tokens] = [params[:reader_token]]
 111     find_object_by_uuid
 112     render layout: false
 113   end
 114
 115   def show_file
 116     # We pipe from arv-get to send the file to the user.  Before we start it,
 117     # we ask the API server if the file actually exists.  This serves two
 118     # purposes: it lets us return a useful status code for common errors, and
 119     # helps us figure out which token to provide to arv-get.
 120     coll = nil
 121     tokens = [Thread.current[:arvados_api_token], params[:reader_token]].compact
 122     usable_token = find_usable_token(tokens) do
 123       coll = Collection.find(params[:uuid])
 124     end
 125     if usable_token.nil?
 126       return  # Response already rendered.
 127     elsif params[:file].nil? or not file_in_collection?(coll, params[:file])
 128       return render_not_found
 129     end
 130     opts = params.merge(arvados_api_token: usable_token)
 131     ext = File.extname(params[:file])
 132     self.response.headers['Content-Type'] =
 133       Rack::Mime::MIME_TYPES[ext] || 'application/octet-stream'
 134     self.response.headers['Content-Length'] = params[:size] if params[:size]
 135     self.response.headers['Content-Disposition'] = params[:disposition] if params[:disposition]
 136     self.response_body = file_enumerator opts
 137   end
 138
 139   def sharing_scopes
 140     ["GET /arvados/v1/collections/#{@object.uuid}", "GET /arvados/v1/collections/#{@object.uuid}/", "GET /arvados/v1/keep_services/accessible"]
 141   end
 142
 143   def search_scopes
 144     begin
 145       ApiClientAuthorization.filter([['scopes', '=', sharing_scopes]]).results
 146     rescue ArvadosApiClient::AccessForbiddenException
 147       nil
 148     end
 149   end
 150
 151   def show
 152     return super if !@object
 153     if current_user
 154       jobs_with = lambda do |conds|
 155         Job.limit(RELATION_LIMIT).where(conds)
 156           .results.sort_by { |j| j.finished_at || j.created_at }
 157       end
 158       @output_of = jobs_with.call(output: @object.uuid)
 159       @log_of = jobs_with.call(log: @object.uuid)
 160       project_links = Link.limit(RELATION_LIMIT).order("modified_at DESC")
 161         .where(head_uuid: @object.uuid, link_class: 'name').results
 162       project_hash = Group.where(uuid: project_links.map(&:tail_uuid)).to_hash
 163       @projects = project_links.map { |link| project_hash[link.tail_uuid] }
 164       @permissions = Link.limit(RELATION_LIMIT).order("modified_at DESC")
 165         .where(head_uuid: @object.uuid, link_class: 'permission',
 166                name: 'can_read').results
 167       @logs = Log.limit(RELATION_LIMIT).order("created_at DESC")
 168         .where(object_uuid: @object.uuid).results
 169       @is_persistent = Link.limit(1)
 170         .where(head_uuid: @object.uuid, tail_uuid: current_user.uuid,
 171                link_class: 'resources', name: 'wants')
 172         .results.any?
 173       @search_sharing = search_scopes
 174     end
 175     @prov_svg = ProvenanceHelper::create_provenance_graph(@object.provenance, "provenance_svg",
 176                                                           {:request => request,
 177                                                             :direction => :bottom_up,
 178                                                             :combine_jobs => :script_only}) rescue nil
 179     @used_by_svg = ProvenanceHelper::create_provenance_graph(@object.used_by, "used_by_svg",
 180                                                              {:request => request,
 181                                                                :direction => :top_down,
 182                                                                :combine_jobs => :script_only,
 183                                                                :pdata_only => true}) rescue nil
 184   end
 185
 186   def sharing_popup
 187     @search_sharing = search_scopes
 188     respond_to do |format|
 189       format.html
 190       format.js
 191     end
 192   end
 193
 194   helper_method :download_link
 195
 196   def download_link
 197     collections_url + "/download/#{@object.uuid}/#{@search_sharing.first.api_token}"
 198   end
 199
 200   def share
 201     a = ApiClientAuthorization.create(scopes: sharing_scopes)
 202     @search_sharing = search_scopes
 203     render 'sharing_popup'
 204   end
 205
 206   def unshare
 207     @search_sharing = search_scopes
 208     @search_sharing.each do |s|
 209       s.destroy
 210     end
 211     @search_sharing = search_scopes
 212     render 'sharing_popup'
 213   end
 214
 215   protected
 216
 217   def find_usable_token(token_list)
 218     # Iterate over every given token to make it the current token and
 219     # yield the given block.
 220     # If the block succeeds, return the token it used.
 221     # Otherwise, render an error response based on the most specific
 222     # error we encounter, and return nil.
 223     most_specific_error = [401]
 224     token_list.each do |api_token|
 225       using_specific_api_token(api_token) do
 226         begin
 227           yield
 228           return api_token
 229         rescue ArvadosApiClient::NotLoggedInException => error
 230           status = 401
 231         rescue => error
 232           status = (error.message =~ /\[API: (\d+)\]$/) ? $1.to_i : nil
 233           raise unless [401, 403, 404].include?(status)
 234         end
 235         if status >= most_specific_error.first
 236           most_specific_error = [status, error]
 237         end
 238       end
 239     end
 240     case most_specific_error.shift
 241     when 401, 403
 242       redirect_to_login
 243     when 404
 244       render_not_found(*most_specific_error)
 245     end
 246     return nil
 247   end
 248
 249   def file_in_collection?(collection, filename)
 250     target = CollectionsHelper.file_path(File.split(filename))
 251     collection.files.each do |file_spec|
 252       return true if (CollectionsHelper.file_path(file_spec) == target)
 253     end
 254     false
 255   end
 256
 257   def file_enumerator(opts)
 258     FileStreamer.new opts
 259   end
 260
 261   class FileStreamer
 262     include ArvadosApiClientHelper
 263     def initialize(opts={})
 264       @opts = opts
 265     end
 266     def each
 267       return unless @opts[:uuid] && @opts[:file]
 268
 269       env = Hash[ENV].dup
 270
 271       require 'uri'
 272       u = URI.parse(arvados_api_client.arvados_v1_base)
 273       env['ARVADOS_API_HOST'] = "#{u.host}:#{u.port}"
 274       env['ARVADOS_API_TOKEN'] = @opts[:arvados_api_token]
 275       env['ARVADOS_API_HOST_INSECURE'] = "true" if Rails.configuration.arvados_insecure_https
 276
 277       IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"],
 278                'rb') do |io|
 279         while buf = io.read(2**16)
 280           yield buf
 281         end
 282       end
 283       Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
 284     end
 285   end
 286 end