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