apps/workbench/app/controllers/collections_controller.rb

   1 class CollectionsController < ApplicationController
   2   skip_before_filter :find_object_by_uuid, :only => [:provenance]
   3   skip_before_filter :check_user_agreements, :only => [:show_file]
   4
   5   def show_pane_list
   6     %w(Files Attributes Metadata Provenance_graph Used_by JSON API)
   7   end
   8   def index
   9     if params[:search].andand.length.andand > 0
  10       tags = Link.where(any: ['contains', params[:search]])
  11       @collections = (Collection.where(uuid: tags.collect(&:head_uuid)) |
  12                       Collection.where(any: ['contains', params[:search]])).
  13         uniq { |c| c.uuid }
  14     else
  15       if params[:limit]
  16         limit = params[:limit].to_i
  17       else
  18         limit = 100
  19       end
  20
  21       if params[:offset]
  22         offset = params[:offset].to_i
  23       else
  24         offset = 0
  25       end
  26
  27       @collections = Collection.limit(limit).offset(offset)
  28     end
  29     @links = Link.limit(1000).
  30       where(head_uuid: @collections.collect(&:uuid))
  31     @collection_info = {}
  32     @collections.each do |c|
  33       @collection_info[c.uuid] = {
  34         tag_links: [],
  35         wanted: false,
  36         wanted_by_me: false,
  37         provenance: [],
  38         links: []
  39       }
  40     end
  41     @links.each do |link|
  42       @collection_info[link.head_uuid] ||= {}
  43       info = @collection_info[link.head_uuid]
  44       case link.link_class
  45       when 'tag'
  46         info[:tag_links] << link
  47       when 'resources'
  48         info[:wanted] = true
  49         info[:wanted_by_me] ||= link.tail_uuid == current_user.uuid
  50       when 'provenance'
  51         info[:provenance] << link.name
  52       end
  53       info[:links] << link
  54     end
  55     @request_url = request.url
  56   end
  57
  58   def show_file
  59     opts = params.merge(arvados_api_token: Thread.current[:arvados_api_token])
  60     if r = params[:file].match(/(\.\w+)/)
  61       ext = r[1]
  62     end
  63     self.response.headers['Content-Type'] =
  64       Rack::Mime::MIME_TYPES[ext] || 'application/octet-stream'
  65     self.response.headers['Content-Length'] = params[:size] if params[:size]
  66     self.response.headers['Content-Disposition'] = params[:disposition] if params[:disposition]
  67     self.response_body = FileStreamer.new opts
  68   end
  69
  70
  71   def show
  72     return super if !@object
  73     @provenance = []
  74     @output2job = {}
  75     @output2colorindex = {}
  76     @sourcedata = {params[:uuid] => {uuid: params[:uuid]}}
  77     @protected = {}
  78
  79     colorindex = -1
  80     any_hope_left = true
  81     while any_hope_left
  82       any_hope_left = false
  83       Job.where(output: @sourcedata.keys).sort_by { |a| a.finished_at || a.created_at }.reverse.each do |job|
  84         if !@output2colorindex[job.output]
  85           any_hope_left = true
  86           @output2colorindex[job.output] = (colorindex += 1) % 10
  87           @provenance << {job: job, output: job.output}
  88           @sourcedata.delete job.output
  89           @output2job[job.output] = job
  90           job.dependencies.each do |new_source_data|
  91             unless @output2colorindex[new_source_data]
  92               @sourcedata[new_source_data] = {uuid: new_source_data}
  93             end
  94           end
  95         end
  96       end
  97     end
  98
  99     Link.where(head_uuid: @sourcedata.keys | @output2job.keys).each do |link|
 100       if link.link_class == 'resources' and link.name == 'wants'
 101         @protected[link.head_uuid] = true
 102       end
 103     end
 104     Link.where(tail_uuid: @sourcedata.keys).each do |link|
 105       if link.link_class == 'data_origin'
 106         @sourcedata[link.tail_uuid][:data_origins] ||= []
 107         @sourcedata[link.tail_uuid][:data_origins] << [link.name, link.head_uuid]
 108       end
 109     end
 110     Collection.where(uuid: @sourcedata.keys).each do |collection|
 111       if @sourcedata[collection.uuid]
 112         @sourcedata[collection.uuid][:collection] = collection
 113       end
 114     end
 115
 116     Collection.where(uuid: @object.uuid).each do |u|
 117       puts request
 118       @prov_svg = ProvenanceHelper::create_provenance_graph(u.provenance, "provenance_svg",
 119                                                             {:request => request,
 120                                                               :direction => :bottom_up,
 121                                                               :combine_jobs => :script_only}) rescue nil
 122       @used_by_svg = ProvenanceHelper::create_provenance_graph(u.used_by, "used_by_svg",
 123                                                                {:request => request,
 124                                                                  :direction => :top_down,
 125                                                                  :combine_jobs => :script_only,
 126                                                                  :pdata_only => true}) rescue nil
 127     end
 128   end
 129
 130   protected
 131   class FileStreamer
 132     def initialize(opts={})
 133       @opts = opts
 134     end
 135     def each
 136       return unless @opts[:uuid] && @opts[:file]
 137       env = Hash[ENV].
 138         merge({
 139                 'ARVADOS_API_HOST' =>
 140                 $arvados_api_client.arvados_v1_base.
 141                 sub(/\/arvados\/v1/, '').
 142                 sub(/^https?:\/\//, ''),
 143                 'ARVADOS_API_TOKEN' =>
 144                 @opts[:arvados_api_token],
 145                 'ARVADOS_API_HOST_INSECURE' =>
 146                 Rails.configuration.arvados_insecure_https ? 'true' : 'false'
 147               })
 148       IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"],
 149                'rb') do |io|
 150         while buf = io.read(2**20)
 151           yield buf
 152         end
 153       end
 154       Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
 155     end
 156   end
 157 end