services/api/test/unit/salvage_collection_test.rb

   1 require 'test_helper'
   2 require 'salvage_collection'
   3
   4 TEST_MANIFEST = ". 341dabea2bd78ad0d6fc3f5b926b450e+85626+Ad391622a17f61e4a254eda85d1ca751c4f368da9@55e076ce 0:85626:brca2-hg19.fa\n. d7321a918923627c972d8f8080c07d29+82570+A22e0a1d9b9bc85c848379d98bedc64238b0b1532@55e076ce 0:82570:brca1-hg19.fa\n"
   5
   6 module SalvageCollection
   7   def self.salvage_collection_arv_put(cmd)
   8     file_contents = File.new(cmd.split[-1], "r").gets
   9
  10     # simulate arv-put error when it is 'user_agreement'
  11     if file_contents.include? 'GNU_General_Public_License'
  12       raise("Error during arv-put")
  13     else
  14       ". " +
  15       Digest::MD5.hexdigest(TEST_MANIFEST) +
  16       " 0:" + TEST_MANIFEST.length.to_s + ":invalid_manifest_text.txt\n"
  17     end
  18   end
  19 end
  20
  21 class SalvageCollectionMockTest < ActiveSupport::TestCase
  22   include SalvageCollection
  23
  24   setup do
  25     set_user_from_auth :admin
  26     # arv-put needs ARV env variables
  27     ENV['ARVADOS_API_HOST'] = 'unused_by_test'
  28     ENV['ARVADOS_API_TOKEN'] = 'unused_by_test'
  29   end
  30
  31   teardown do
  32     ENV['ARVADOS_API_HOST'] = ''
  33     ENV['ARVADOS_API_TOKEN'] = ''
  34   end
  35
  36   test "salvage test collection" do
  37     # create a collection to test salvaging
  38     src_collection = Collection.new name: "test collection", manifest_text: TEST_MANIFEST
  39     src_collection.save!
  40
  41     # salvage this collection
  42     SalvageCollection.salvage_collection src_collection.uuid, 'test salvage collection - see #6277, #6859'
  43
  44     # verify the updated src_collection data
  45     updated_src_collection = Collection.find_by_uuid src_collection.uuid
  46     updated_name = updated_src_collection.name
  47     assert_equal true, updated_name.include?(src_collection.name)
  48
  49     match = updated_name.match /^test collection.*salvaged data at (.*)\)$/
  50     assert_not_nil match
  51     assert_not_nil match[1]
  52     assert_empty updated_src_collection.manifest_text
  53
  54     # match[1] is the uuid of the new collection created from src_collection's salvaged data
  55     # use this to get the new collection and verify
  56     new_collection = Collection.find_by_uuid match[1]
  57     match = new_collection.name.match /^salvaged from (.*),.*/
  58     assert_not_nil match
  59     assert_equal src_collection.uuid, match[1]
  60
  61     # verify the new collection's manifest format
  62     match = new_collection.manifest_text.match /^. (.*) (.*):invalid_manifest_text.txt\n. (.*) (.*):salvaged_data/
  63     assert_not_nil match
  64   end
  65
  66   test "salvage collection with no uuid required argument" do
  67     e = assert_raises RuntimeError do
  68       SalvageCollection.salvage_collection nil
  69     end
  70   end
  71
  72   test "salvage collection with bogus uuid" do
  73     e = assert_raises RuntimeError do
  74       SalvageCollection.salvage_collection 'bogus-uuid'
  75     end
  76     assert_equal "No collection found for bogus-uuid.", e.message
  77   end
  78
  79   test "salvage collection with no env ARVADOS_API_HOST" do
  80     e = assert_raises RuntimeError do
  81       ENV['ARVADOS_API_HOST'] = ''
  82       ENV['ARVADOS_API_TOKEN'] = ''
  83       SalvageCollection.salvage_collection collections('user_agreement').uuid
  84     end
  85     assert_equal "ARVADOS environment variables missing. Please set your admin user credentials as ARVADOS environment variables.", e.message
  86   end
  87
  88   test "salvage collection with error during arv-put" do
  89     # try to salvage collection while mimicking error during arv-put
  90     e = assert_raises RuntimeError do
  91       SalvageCollection.salvage_collection collections('user_agreement').uuid
  92     end
  93     assert_equal "Error during arv-put", e.message
  94   end
  95
  96   # This test has two invalid locators:
  97   #     341dabea2bd78ad0d6fc3f5b926b450e+abc
  98   #     341dabea2bd78ad0d6fc3f5b926b450e
  99   # These locators should be preserved in salvaged_data
 100   test "invalid locators dropped during salvaging" do
 101     manifest = ". 341dabea2bd78ad0d6fc3f5b926b450e+abc 341dabea2bd78ad0d6fc3f5b926abcdf 0:85626:brca2-hg19.fa\n. 341dabea2bd78ad0d6fc3f5b926b450e+1000 0:1000:brca-hg19.fa\n . d7321a918923627c972d8f8080c07d29+2000+A22e0a1d9b9bc85c848379d98bedc64238b0b1532@55e076ce 0:2000:brca1-hg19.fa\n"
 102
 103     # salvage this collection
 104     locator_data = SalvageCollection.salvage_collection_locator_data manifest
 105     assert_equal true, locator_data[0].size.eql?(4)
 106     assert_equal false, locator_data[0].include?("341dabea2bd78ad0d6fc3f5b926b450e+abc")
 107     assert_equal true, locator_data[0].include?("341dabea2bd78ad0d6fc3f5b926b450e")
 108     assert_equal true, locator_data[0].include?("341dabea2bd78ad0d6fc3f5b926abcdf")
 109     assert_equal true, locator_data[0].include?("341dabea2bd78ad0d6fc3f5b926b450e+1000")
 110     assert_equal true, locator_data[0].include?("d7321a918923627c972d8f8080c07d29+2000")
 111     assert_equal true, locator_data[1].eql?(1000 + 2000)   # size
 112   end
 113 end