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