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 show
 124     return super if !@object
 125     if current_user
 126       jobs_with = lambda do |conds|
 127         Job.limit(RELATION_LIMIT).where(conds)
 128           .results.sort_by { |j| j.finished_at || j.created_at }
 129       end
 130       @output_of = jobs_with.call(output: @object.uuid)
 131       @log_of = jobs_with.call(log: @object.uuid)
 132       folder_links = Link.limit(RELATION_LIMIT).order("modified_at DESC")
 133         .where(head_uuid: @object.uuid, link_class: 'name').results
 134       folder_hash = Group.where(uuid: folder_links.map(&:tail_uuid)).to_hash
 135       @folders = folder_links.map { |link| folder_hash[link.tail_uuid] }
 136       @permissions = Link.limit(RELATION_LIMIT).order("modified_at DESC")
 137         .where(head_uuid: @object.uuid, link_class: 'permission',
 138                name: 'can_read').results
 139       @logs = Log.limit(RELATION_LIMIT).order("created_at DESC")
 140         .where(object_uuid: @object.uuid).results
 141       @is_persistent = Link.limit(1)
 142         .where(head_uuid: @object.uuid, tail_uuid: current_user.uuid,
 143                link_class: 'resources', name: 'wants')
 144         .results.any?
 145     end
 146     @prov_svg = ProvenanceHelper::create_provenance_graph(@object.provenance, "provenance_svg",
 147                                                           {:request => request,
 148                                                             :direction => :bottom_up,
 149                                                             :combine_jobs => :script_only}) rescue nil
 150     @used_by_svg = ProvenanceHelper::create_provenance_graph(@object.used_by, "used_by_svg",
 151                                                              {:request => request,
 152                                                                :direction => :top_down,
 153                                                                :combine_jobs => :script_only,
 154                                                                :pdata_only => true}) rescue nil
 155   end
 156
 157   protected
 158
 159   def find_usable_token(token_list)
 160     # Iterate over every given token to make it the current token and
 161     # yield the given block.
 162     # If the block succeeds, return the token it used.
 163     # Otherwise, render an error response based on the most specific
 164     # error we encounter, and return nil.
 165     most_specific_error = [401]
 166     token_list.each do |api_token|
 167       using_specific_api_token(api_token) do
 168         begin
 169           yield
 170           return api_token
 171         rescue ArvadosApiClient::NotLoggedInException => error
 172           status = 401
 173         rescue => error
 174           status = (error.message =~ /\[API: (\d+)\]$/) ? $1.to_i : nil
 175           raise unless [401, 403, 404].include?(status)
 176         end
 177         if status >= most_specific_error.first
 178           most_specific_error = [status, error]
 179         end
 180       end
 181     end
 182     case most_specific_error.shift
 183     when 401, 403
 184       redirect_to_login
 185     when 404
 186       render_not_found(*most_specific_error)
 187     end
 188     return nil
 189   end
 190
 191   def file_in_collection?(collection, filename)
 192     target = CollectionsHelper.file_path(File.split(filename))
 193     collection.files.each do |file_spec|
 194       return true if (CollectionsHelper.file_path(file_spec) == target)
 195     end
 196     false
 197   end
 198
 199   def file_enumerator(opts)
 200     FileStreamer.new opts
 201   end
 202
 203   class FileStreamer
 204     include ArvadosApiClientHelper
 205     def initialize(opts={})
 206       @opts = opts
 207     end
 208     def each
 209       return unless @opts[:uuid] && @opts[:file]
 210
 211       env = Hash[ENV].dup
 212
 213       require 'uri'
 214       u = URI.parse(arvados_api_client.arvados_v1_base)
 215       env['ARVADOS_API_HOST'] = "#{u.host}:#{u.port}"
 216       env['ARVADOS_API_TOKEN'] = @opts[:arvados_api_token]
 217       env['ARVADOS_API_HOST_INSECURE'] = "true" if Rails.configuration.arvados_insecure_https
 218
 219       IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"],
 220                'rb') do |io|
 221         while buf = io.read(2**16)
 222           yield buf
 223         end
 224       end
 225       Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
 226     end
 227   end
 228 end