apps/workbench/app/controllers/collections_controller.rb

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