+# 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"
# This invalid manifest_text has the following flaws:
# Missing stream name with locator in it's place
-# Two invalid locators:
+# Invalid locators:
+# foofaafaafaabd78ad0d6fc3f5b926b450e+foo
+# bar-baabaabaabd78ad0d6fc3f5b926b450e
+# bad12345dae58ad0d6fc3f5b926b450e+
# 341dabea2bd78ad0d6fc3f5b926b450e+abc
-# 341dabea2bd78ad0d6fc3f5b926b450e
-# Expectation: These locators are preserved in salvaged_data
-BAD_MANIFEST = "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"
-
-# Mock arv_put
-module SalvageCollection
- def self.salvage_collection_arv_put(cmd)
- file_contents = File.new(cmd.split[-1], "r").gets
-
- # simulate arv-put error when it is 'user_agreement'
- if file_contents.include? 'GNU_General_Public_License'
- raise("Error during arv-put")
- else
- ". " +
- Digest::MD5.hexdigest(TEST_MANIFEST) + "+" + TEST_MANIFEST.length.to_s +
- " 0:" + TEST_MANIFEST.length.to_s + ":invalid_manifest_text.txt\n"
- end
- end
-end
+# 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
# 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_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 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
# 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
- e = assert_raises RuntimeError do
- SalvageCollection.salvage_collection nil
+ assert_raises RuntimeError do
+ salvage_collection nil
end
end
test "salvage collection with bogus uuid" do
e = assert_raises RuntimeError do
- SalvageCollection.salvage_collection 'bogus-uuid'
+ salvage_collection 'bogus-uuid'
end
assert_equal "No collection found for bogus-uuid.", e.message
end
e = assert_raises RuntimeError do
ENV['ARVADOS_API_HOST'] = ''
ENV['ARVADOS_API_TOKEN'] = ''
- SalvageCollection.salvage_collection collections('user_agreement').uuid
+ 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
- SalvageCollection.salvage_collection collections('user_agreement').uuid
+ salvage_collection collections('user_agreement').uuid
end
- assert_equal "Error during arv-put", e.message
+ 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
- # Two invalid locators:
+ # Invalid locators:
+ # foo-faafaafaabd78ad0d6fc3f5b926b450e+foo
+ # bar-baabaabaabd78ad0d6fc3f5b926b450e
+ # bad12345dae58ad0d6fc3f5b926b450e+
# 341dabea2bd78ad0d6fc3f5b926b450e+abc
- # 341dabea2bd78ad0d6fc3f5b926b450e
- # Expectation: These locators are preserved in salvaged_data
+ # 341dabea2bd78ad0d6fc3f5b926abcdf
+ # Expectation: All these locators are preserved in salvaged_data
test "invalid locators preserved during salvaging" do
- locator_data = SalvageCollection.salvage_collection_locator_data BAD_MANIFEST
- assert_equal true, locator_data[0].size.eql?(4)
- assert_equal false, locator_data[0].include?("341dabea2bd78ad0d6fc3f5b926b450e+abc")
- assert_equal true, locator_data[0].include?("341dabea2bd78ad0d6fc3f5b926b450e")
- assert_equal true, locator_data[0].include?("341dabea2bd78ad0d6fc3f5b926abcdf")
- assert_equal true, locator_data[0].include?("abcdabea2bd78ad0d6fc3f5b926b450e+1000")
- assert_equal true, locator_data[0].include?("d7321a918923627c972d8f8080c07d29+2000")
- assert_equal true, locator_data[1].eql?(1000 + 2000) # size
+ 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
src_collection.save!(validate: false)
# 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
# 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 includes the bad locators
- match = new_collection.manifest_text.match /^. (.*) (.*):invalid_manifest_text.txt\n. (.*) (.*):salvaged_data/
- assert_not_nil match
- assert_includes(new_collection.manifest_text, ". 341dabea2bd78ad0d6fc3f5b926b450e 341dabea2bd78ad0d6fc3f5b926abcdf abcdabea2bd78ad0d6fc3f5b926b450e+1000 d7321a918923627c972d8f8080c07d29+2000 0:3000:salvaged_data")
+ 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
projects / arvados.git / blobdiff