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