X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/3987bcc3f5f6acf9207e94049561c632b454f38a..be66896514a5dccf6364a414d44391a3015592c5:/services/api/test/unit/salvage_collection_test.rb

diff --git a/services/api/test/unit/salvage_collection_test.rb b/services/api/test/unit/salvage_collection_test.rb
index 4cc5378073..89d97f6fd1 100644
--- a/services/api/test/unit/salvage_collection_test.rb
+++ b/services/api/test/unit/salvage_collection_test.rb
@@ -1,21 +1,25 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
 require 'test_helper'
 require 'salvage_collection'
+require 'shellwords'
 
+# Valid manifest_text
 TEST_MANIFEST = ". 341dabea2bd78ad0d6fc3f5b926b450e+85626+Ad391622a17f61e4a254eda85d1ca751c4f368da9@55e076ce 0:85626:brca2-hg19.fa\n. d7321a918923627c972d8f8080c07d29+82570+A22e0a1d9b9bc85c848379d98bedc64238b0b1532@55e076ce 0:82570:brca1-hg19.fa\n"
+TEST_MANIFEST_STRIPPED = ". 341dabea2bd78ad0d6fc3f5b926b450e+85626 0:85626:brca2-hg19.fa\n. d7321a918923627c972d8f8080c07d29+82570 0:82570:brca1-hg19.fa\n"
 
-module Kernel
-  def `(cmd)    # override kernel ` method
-    if cmd.include? 'arv-put'
-      ". " +
-      Digest::MD5.hexdigest(TEST_MANIFEST) +
-      " 0:" + TEST_MANIFEST.length.to_s + ":invalid_manifest_text.txt\n"
-    end
-  end
-
-  def exit code
-    raise "Exit code #{code}" if code != 0
-  end
-end
+# This invalid manifest_text has the following flaws:
+#   Missing stream name with locator in it's place
+#   Invalid locators:
+#     foofaafaafaabd78ad0d6fc3f5b926b450e+foo
+#     bar-baabaabaabd78ad0d6fc3f5b926b450e
+#     bad12345dae58ad0d6fc3f5b926b450e+
+#     341dabea2bd78ad0d6fc3f5b926b450e+abc
+#     341dabea2bd78ad0d6fc3f5b926abcdf
+# Expectation: All these locators are preserved in salvaged_data
+BAD_MANIFEST = "faafaafaabd78ad0d6fc3f5b926b450e+foo bar-baabaabaabd78ad0d6fc3f5b926b450e_bad12345dae58ad0d6fc3f5b926b450e+ 341dabea2bd78ad0d6fc3f5b926b450e+abc 341dabea2bd78ad0d6fc3f5b926abcdf 0:85626:brca2-hg19.fa\n. abcdabea2bd78ad0d6fc3f5b926b450e+1000 0:1000:brca-hg19.fa\n. d7321a918923627c972d8f8080c07d29+2000+A22e0a1d9b9bc85c848379d98bedc64238b0b1532@55e076ce 0:2000:brca1-hg19.fa\n"
 
 class SalvageCollectionTest < ActiveSupport::TestCase
   include SalvageCollection
@@ -25,22 +29,42 @@ class SalvageCollectionTest < ActiveSupport::TestCase
     # arv-put needs ARV env variables
     ENV['ARVADOS_API_HOST'] = 'unused_by_test'
     ENV['ARVADOS_API_TOKEN'] = 'unused_by_test'
+    @backtick_mock_failure = false
+  end
+
+  teardown do
+    ENV['ARVADOS_API_HOST'] = ''
+    ENV['ARVADOS_API_TOKEN'] = ''
+  end
+
+  def ` cmd # mock Kernel `
+    assert_equal 'arv-put', cmd.shellsplit[0]
+    if @backtick_mock_failure
+      # run a process so $? indicates failure
+      return super 'false'
+    end
+    # run a process so $? indicates success
+    super 'true'
+    file_contents = File.open(cmd.shellsplit[-1], "r").read
+    ". " +
+      Digest::MD5.hexdigest(file_contents) + "+" + file_contents.length.to_s +
+      " 0:" + file_contents.length.to_s + ":invalid_manifest_text.txt\n"
   end
 
-  test "salvage test collection" do
+  test "salvage test collection with valid manifest text" do
     # create a collection to test salvaging
     src_collection = Collection.new name: "test collection", manifest_text: TEST_MANIFEST
     src_collection.save!
 
     # salvage this collection
-    SalvageCollection.salvage_collection src_collection.uuid, 'test salvage collection - see #6277, #6859'
+    salvage_collection src_collection.uuid, 'test salvage collection - see #6277, #6859'
 
     # verify the updated src_collection data
     updated_src_collection = Collection.find_by_uuid src_collection.uuid
     updated_name = updated_src_collection.name
     assert_equal true, updated_name.include?(src_collection.name)
 
-    match = updated_name.match /^test collection.*salvaged data at (.*)\)$/
+    match = updated_name.match(/^test collection.*salvaged data at (.*)\)$/)
     assert_not_nil match
     assert_not_nil match[1]
     assert_empty updated_src_collection.manifest_text
@@ -48,35 +72,98 @@ class SalvageCollectionTest < ActiveSupport::TestCase
     # match[1] is the uuid of the new collection created from src_collection's salvaged data
     # use this to get the new collection and verify
     new_collection = Collection.find_by_uuid match[1]
-    match = new_collection.name.match /^salvaged from (.*),.*/
+    match = new_collection.name.match(/^salvaged from (.*),.*/)
     assert_not_nil match
     assert_equal src_collection.uuid, match[1]
 
     # verify the new collection's manifest format
-    match = new_collection.manifest_text.match /^. (.*) (.*):invalid_manifest_text.txt\n. (.*) (.*):salvaged_data/
-    assert_not_nil match
+    expected_manifest = ". " + Digest::MD5.hexdigest(TEST_MANIFEST_STRIPPED) + "+" +
+      TEST_MANIFEST_STRIPPED.length.to_s + " 0:" + TEST_MANIFEST_STRIPPED.length.to_s +
+      ":invalid_manifest_text.txt\n. 341dabea2bd78ad0d6fc3f5b926b450e+85626 d7321a918923627c972d8f8080c07d29+82570 0:168196:salvaged_data\n"
+    assert_equal expected_manifest, new_collection.manifest_text
   end
 
   test "salvage collection with no uuid required argument" do
-    status = SalvageCollection.salvage_collection nil
-    assert_equal false, status
+    assert_raises RuntimeError do
+      salvage_collection nil
+    end
   end
 
   test "salvage collection with bogus uuid" do
-    status = SalvageCollection.salvage_collection 'bogus-uuid'
-    assert_equal false, status
+    e = assert_raises RuntimeError do
+      salvage_collection 'bogus-uuid'
+    end
+    assert_equal "No collection found for bogus-uuid.", e.message
   end
 
   test "salvage collection with no env ARVADOS_API_HOST" do
-    exited = false
-    begin
+    e = assert_raises RuntimeError do
       ENV['ARVADOS_API_HOST'] = ''
       ENV['ARVADOS_API_TOKEN'] = ''
-      SalvageCollection.salvage_collection collections('user_agreement').uuid
-    rescue => e
-      assert_equal "Exit code 1", e.message
-      exited = true
+      salvage_collection collections('user_agreement').uuid
+    end
+    assert_equal "ARVADOS environment variables missing. Please set your admin user credentials as ARVADOS environment variables.", e.message
+  end
+
+  test "salvage collection with error during arv-put" do
+    # try to salvage collection while mimicking error during arv-put
+    @backtick_mock_failure = true
+    e = assert_raises RuntimeError do
+      salvage_collection collections('user_agreement').uuid
     end
-    assert_equal true, exited
+    assert_match(/Error during arv-put: pid \d+ exit \d+ \(cmd was \"arv-put .*\"\)/, e.message)
+  end
+
+  # This test uses BAD_MANIFEST, which has the following flaws:
+  #   Missing stream name with locator in it's place
+  #   Invalid locators:
+  #     foo-faafaafaabd78ad0d6fc3f5b926b450e+foo
+  #     bar-baabaabaabd78ad0d6fc3f5b926b450e
+  #     bad12345dae58ad0d6fc3f5b926b450e+
+  #     341dabea2bd78ad0d6fc3f5b926b450e+abc
+  #     341dabea2bd78ad0d6fc3f5b926abcdf
+  # Expectation: All these locators are preserved in salvaged_data
+  test "invalid locators preserved during salvaging" do
+    locator_data = salvage_collection_locator_data BAD_MANIFEST
+    assert_equal \
+    ["faafaafaabd78ad0d6fc3f5b926b450e",
+     "baabaabaabd78ad0d6fc3f5b926b450e",
+     "bad12345dae58ad0d6fc3f5b926b450e",
+     "341dabea2bd78ad0d6fc3f5b926b450e",
+     "341dabea2bd78ad0d6fc3f5b926abcdf",
+     "abcdabea2bd78ad0d6fc3f5b926b450e+1000",
+     "d7321a918923627c972d8f8080c07d29+2000",
+    ], locator_data[0]
+    assert_equal 1000+2000, locator_data[1]
+  end
+
+  test "salvage a collection with invalid manifest text" do
+    # create a collection to test salvaging
+    src_collection = Collection.new name: "test collection", manifest_text: BAD_MANIFEST, owner_uuid: 'zzzzz-tpzed-000000000000000'
+    src_collection.save!(validate: false)
+
+    # salvage this collection
+    salvage_collection src_collection.uuid, 'test salvage collection - see #6277, #6859'
+
+    # verify the updated src_collection data
+    updated_src_collection = Collection.find_by_uuid src_collection.uuid
+    updated_name = updated_src_collection.name
+    assert_equal true, updated_name.include?(src_collection.name)
+
+    match = updated_name.match(/^test collection.*salvaged data at (.*)\)$/)
+    assert_not_nil match
+    assert_not_nil match[1]
+    assert_empty updated_src_collection.manifest_text
+
+    # match[1] is the uuid of the new collection created from src_collection's salvaged data
+    # use this to get the new collection and verify
+    new_collection = Collection.find_by_uuid match[1]
+    match = new_collection.name.match(/^salvaged from (.*),.*/)
+    assert_not_nil match
+    assert_equal src_collection.uuid, match[1]
+    # verify the new collection's manifest includes the bad locators
+    expected_manifest = ". " + Digest::MD5.hexdigest(BAD_MANIFEST) + "+" + BAD_MANIFEST.length.to_s +
+      " 0:" + BAD_MANIFEST.length.to_s + ":invalid_manifest_text.txt\n. faafaafaabd78ad0d6fc3f5b926b450e baabaabaabd78ad0d6fc3f5b926b450e bad12345dae58ad0d6fc3f5b926b450e 341dabea2bd78ad0d6fc3f5b926b450e 341dabea2bd78ad0d6fc3f5b926abcdf abcdabea2bd78ad0d6fc3f5b926b450e+1000 d7321a918923627c972d8f8080c07d29+2000 0:3000:salvaged_data\n"
+    assert_equal expected_manifest, new_collection.manifest_text
   end
 end