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
 108     render_index
 109   end
 110
 111   def show_file_links
 112     Thread.current[:reader_tokens] = [params[:reader_token]]
 113     find_object_by_uuid
 114     render layout: false
 115   end
 116
 117   def show_file
 118     # We pipe from arv-get to send the file to the user.  Before we start it,
 119     # we ask the API server if the file actually exists.  This serves two
 120     # purposes: it lets us return a useful status code for common errors, and
 121     # helps us figure out which token to provide to arv-get.
 122     coll = nil
 123     tokens = [Thread.current[:arvados_api_token], params[:reader_token]].compact
 124     usable_token = find_usable_token(tokens) do
 125       coll = Collection.find(params[:uuid])
 126     end
 127     if usable_token.nil?
 128       return  # Response already rendered.
 129     elsif params[:file].nil? or not file_in_collection?(coll, params[:file])
 130       return render_not_found
 131     end
 132     opts = params.merge(arvados_api_token: usable_token)
 133     ext = File.extname(params[:file])
 134     self.response.headers['Content-Type'] =
 135       Rack::Mime::MIME_TYPES[ext] || 'application/octet-stream'
 136     self.response.headers['Content-Length'] = params[:size] if params[:size]
 137     self.response.headers['Content-Disposition'] = params[:disposition] if params[:disposition]
 138     self.response_body = file_enumerator opts
 139   end
 140
 141   def sharing_scopes
 142     ["GET /arvados/v1/collections/#{@object.uuid}", "GET /arvados/v1/collections/#{@object.uuid}/", "GET /arvados/v1/keep_services/accessible"]
 143   end
 144
 145   def search_scopes
 146     begin
 147       ApiClientAuthorization.filter([['scopes', '=', sharing_scopes]]).results
 148     rescue ArvadosApiClient::AccessForbiddenException
 149       nil
 150     end
 151   end
 152
 153   def show
 154     return super if !@object
 155     if current_user
 156       jobs_with = lambda do |conds|
 157         Job.limit(RELATION_LIMIT).where(conds)
 158           .results.sort_by { |j| j.finished_at || j.created_at }
 159       end
 160       @output_of = jobs_with.call(output: @object.uuid)
 161       @log_of = jobs_with.call(log: @object.uuid)
 162       @project_links = Link.limit(RELATION_LIMIT).order("modified_at DESC")
 163         .where(head_uuid: @object.uuid, link_class: 'name').results
 164       project_hash = Group.where(uuid: @project_links.map(&:tail_uuid)).to_hash
 165       @projects = @project_links.map { |link| project_hash[link.tail_uuid] }
 166       @permissions = Link.limit(RELATION_LIMIT).order("modified_at DESC")
 167         .where(head_uuid: @object.uuid, link_class: 'permission',
 168                name: 'can_read').results
 169       @logs = Log.limit(RELATION_LIMIT).order("created_at DESC")
 170         .where(object_uuid: @object.uuid).results
 171       @is_persistent = Link.limit(1)
 172         .where(head_uuid: @object.uuid, tail_uuid: current_user.uuid,
 173                link_class: 'resources', name: 'wants')
 174         .results.any?
 175       @search_sharing = search_scopes
 176     end
 177     @prov_svg = ProvenanceHelper::create_provenance_graph(@object.provenance, "provenance_svg",
 178                                                           {:request => request,
 179                                                             :direction => :bottom_up,
 180                                                             :combine_jobs => :script_only}) rescue nil
 181     @used_by_svg = ProvenanceHelper::create_provenance_graph(@object.used_by, "used_by_svg",
 182                                                              {:request => request,
 183                                                                :direction => :top_down,
 184                                                                :combine_jobs => :script_only,
 185                                                                :pdata_only => true}) rescue nil
 186
 187     super
 188   end
 189
 190   def sharing_popup
 191     @search_sharing = search_scopes
 192     respond_to do |format|
 193       format.html
 194       format.js
 195     end
 196   end
 197
 198   helper_method :download_link
 199
 200   def download_link
 201     collections_url + "/download/#{@object.uuid}/#{@search_sharing.first.api_token}"
 202   end
 203
 204   def share
 205     a = ApiClientAuthorization.create(scopes: sharing_scopes)
 206     @search_sharing = search_scopes
 207     render 'sharing_popup'
 208   end
 209
 210   def unshare
 211     @search_sharing = search_scopes
 212     @search_sharing.each do |s|
 213       s.destroy
 214     end
 215     @search_sharing = search_scopes
 216     render 'sharing_popup'
 217   end
 218
 219   protected
 220
 221   def find_usable_token(token_list)
 222     # Iterate over every given token to make it the current token and
 223     # yield the given block.
 224     # If the block succeeds, return the token it used.
 225     # Otherwise, render an error response based on the most specific
 226     # error we encounter, and return nil.
 227     most_specific_error = [401]
 228     token_list.each do |api_token|
 229       using_specific_api_token(api_token) do
 230         begin
 231           yield
 232           return api_token
 233         rescue ArvadosApiClient::NotLoggedInException => error
 234           status = 401
 235         rescue => error
 236           status = (error.message =~ /\[API: (\d+)\]$/) ? $1.to_i : nil
 237           raise unless [401, 403, 404].include?(status)
 238         end
 239         if status >= most_specific_error.first
 240           most_specific_error = [status, error]
 241         end
 242       end
 243     end
 244     case most_specific_error.shift
 245     when 401, 403
 246       redirect_to_login
 247     when 404
 248       render_not_found(*most_specific_error)
 249     end
 250     return nil
 251   end
 252
 253   def file_in_collection?(collection, filename)
 254     target = CollectionsHelper.file_path(File.split(filename))
 255     collection.files.each do |file_spec|
 256       return true if (CollectionsHelper.file_path(file_spec) == target)
 257     end
 258     false
 259   end
 260
 261   def file_enumerator(opts)
 262     FileStreamer.new opts
 263   end
 264
 265   class FileStreamer
 266     include ArvadosApiClientHelper
 267     def initialize(opts={})
 268       @opts = opts
 269     end
 270     def each
 271       return unless @opts[:uuid] && @opts[:file]
 272
 273       env = Hash[ENV].dup
 274
 275       require 'uri'
 276       u = URI.parse(arvados_api_client.arvados_v1_base)
 277       env['ARVADOS_API_HOST'] = "#{u.host}:#{u.port}"
 278       env['ARVADOS_API_TOKEN'] = @opts[:arvados_api_token]
 279       env['ARVADOS_API_HOST_INSECURE'] = "true" if Rails.configuration.arvados_insecure_https
 280
 281       IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"],
 282                'rb') do |io|
 283         while buf = io.read(2**16)
 284           yield buf
 285         end
 286       end
 287       Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
 288     end
 289   end
 290 end