apps/workbench/app/controllers/actions_controller.rb

   1 class ActionsController < ApplicationController
   2
   3   skip_before_filter :find_object_by_uuid, only: :post
   4
   5   def combine_selected_files_into_collection
   6     lst = []
   7     files = []
   8     params["selection"].each do |s|
   9       m = CollectionsHelper.match(s)
  10       if m and m[1] and m[2]
  11         lst.append(m[1] + m[2])
  12         files.append(m)
  13       end
  14     end
  15
  16     collections = Collection.where(uuid: lst)
  17
  18     chash = {}
  19     collections.each do |c|
  20       c.reload()
  21       chash[c.uuid] = c
  22     end
  23
  24     combined = ""
  25     files.each do |m|
  26       mt = chash[m[1]+m[2]].manifest_text
  27       if m[4]
  28         IO.popen(['arv-normalize', '--extract', m[4][1..-1]], 'w+b') do |io|
  29           io.write mt
  30           io.close_write
  31           while buf = io.read(2**20)
  32             combined += buf
  33           end
  34         end
  35       else
  36         combined += chash[m[1]+m[2]].manifest_text
  37       end
  38     end
  39
  40     normalized = ''
  41     IO.popen(['arv-normalize'], 'w+b') do |io|
  42       io.write combined
  43       io.close_write
  44       while buf = io.read(2**20)
  45         normalized += buf
  46       end
  47     end
  48
  49     require 'digest/md5'
  50
  51     d = Digest::MD5.new()
  52     d << normalized
  53     newuuid = "#{d.hexdigest}+#{normalized.length}"
  54
  55     env = Hash[ENV].
  56       merge({
  57               'ARVADOS_API_HOST' =>
  58               $arvados_api_client.arvados_v1_base.
  59               sub(/\/arvados\/v1/, '').
  60               sub(/^https?:\/\//, ''),
  61               'ARVADOS_API_TOKEN' => Thread.current[:arvados_api_token],
  62               'ARVADOS_API_HOST_INSECURE' =>
  63               Rails.configuration.arvados_insecure_https ? 'true' : 'false'
  64             })
  65
  66     IO.popen([env, 'arv-put', '--raw'], 'w+b') do |io|
  67       io.write normalized
  68       io.close_write
  69       while buf = io.read(2**20)
  70
  71       end
  72     end
  73
  74     newc = Collection.new({:uuid => newuuid, :manifest_text => normalized})
  75     newc.save!
  76
  77     chash.each do |k,v|
  78       l = Link.new({
  79                      tail_uuid: k,
  80                      head_uuid: newuuid,
  81                      link_class: "provenance",
  82                      name: "provided"
  83                    })
  84       l.save!
  85     end
  86
  87     redirect_to controller: 'collections', action: :show, id: newc.uuid
  88   end
  89
  90   def post
  91     if params["combine_selected_files_into_collection"]
  92       combine_selected_files_into_collection
  93     else
  94       redirect_to :back
  95     end
  96   end
  97 end