[ARVADOS] updated: 9259c169b6254ea581fcdcb18e1cdbe9b9fbea1e
git at public.curoverse.com
git at public.curoverse.com
Thu Aug 27 10:46:16 EDT 2015
Summary of changes:
services/api/lib/salvage_collection.rb | 6 +--
services/api/test/unit/salvage_collection_test.rb | 48 ++++++++++++-----------
2 files changed, 28 insertions(+), 26 deletions(-)
via 9259c169b6254ea581fcdcb18e1cdbe9b9fbea1e (commit)
from 7fc67e3f9bfd12058e6f3d86d995704ed8962a8b (commit)
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commit 9259c169b6254ea581fcdcb18e1cdbe9b9fbea1e
Author: Tom Clegg <tom at curoverse.com>
Date: Thu Aug 27 10:45:33 2015 -0400
6859: Fix up module usage, mock backtick to test arv-put error handling.
diff --git a/services/api/lib/salvage_collection.rb b/services/api/lib/salvage_collection.rb
index 86c95c6..79a2d58 100755
--- a/services/api/lib/salvage_collection.rb
+++ b/services/api/lib/salvage_collection.rb
@@ -14,7 +14,7 @@ module SalvageCollection
require 'tempfile'
require 'shellwords'
- def self.salvage_collection_arv_put cmd
+ def salvage_collection_arv_put cmd
new_manifest = %x(#{cmd})
if $?.success?
new_manifest
@@ -25,7 +25,7 @@ module SalvageCollection
# Get all the locators from the original manifest
LOCATOR_REGEXP = /((.*))?([[:xdigit:]]{32})(\+(.*))?\z/
- def self.salvage_collection_locator_data manifest
+ def salvage_collection_locator_data manifest
locators = []
size = 0
manifest.each_line do |line|
@@ -50,7 +50,7 @@ module SalvageCollection
return [locators, size]
end
- def self.salvage_collection uuid, reason='salvaged - see #6277, #6859'
+ def salvage_collection uuid, reason='salvaged - see #6277, #6859'
act_as_system_user do
if !ENV['ARVADOS_API_TOKEN'].present? or !ENV['ARVADOS_API_HOST'].present?
raise "ARVADOS environment variables missing. Please set your admin user credentials as ARVADOS environment variables."
diff --git a/services/api/test/unit/salvage_collection_test.rb b/services/api/test/unit/salvage_collection_test.rb
index 96b2c3e..47abe5a 100644
--- a/services/api/test/unit/salvage_collection_test.rb
+++ b/services/api/test/unit/salvage_collection_test.rb
@@ -1,5 +1,6 @@
require 'test_helper'
require 'salvage_collection'
+require 'shellwords'
# Valid manifest_text
TEST_MANIFEST = ". 341dabea2bd78ad0d6fc3f5b926b450e+85626+Ad391622a17f61e4a254eda85d1ca751c4f368da9 at 55e076ce 0:85626:brca2-hg19.fa\n. d7321a918923627c972d8f8080c07d29+82570+A22e0a1d9b9bc85c848379d98bedc64238b0b1532 at 55e076ce 0:82570:brca1-hg19.fa\n"
@@ -16,21 +17,6 @@ TEST_MANIFEST_STRIPPED = ". 341dabea2bd78ad0d6fc3f5b926b450e+85626 0:85626:brca2
# Expectation: All these locators are preserved in salvaged_data
BAD_MANIFEST = "faaaafaafaafaabd78ad0d6fc3f5b926b450e+foo bar-baabaabaabd78ad0d6fc3f5b926b450e bad12345dae58ad0d6fc3f5b926b450e+ 341dabea2bd78ad0d6fc3f5b926b450e+abc 341dabea2bd78ad0d6fc3f5b926abcdf 0:85626:brca2-hg19.fa\n. abcdabea2bd78ad0d6fc3f5b926b450e+1000 0:1000:brca-hg19.fa\n. d7321a918923627c972d8f8080c07d29+2000+A22e0a1d9b9bc85c848379d98bedc64238b0b1532 at 55e076ce 0:2000:brca1-hg19.fa\n"
-# Mock arv_put
-module SalvageCollection
- def self.salvage_collection_arv_put(cmd)
- file_contents = File.open(cmd.split[-1], "r").read
- # 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(file_contents) + "+" + file_contents.length.to_s +
- " 0:" + file_contents.length.to_s + ":invalid_manifest_text.txt\n"
- end
- end
-end
-
class SalvageCollectionTest < ActiveSupport::TestCase
include SalvageCollection
@@ -39,6 +25,7 @@ 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
@@ -46,13 +33,27 @@ class SalvageCollectionTest < ActiveSupport::TestCase
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
@@ -80,13 +81,13 @@ class SalvageCollectionTest < ActiveSupport::TestCase
test "salvage collection with no uuid required argument" do
e = assert_raises RuntimeError do
- SalvageCollection.salvage_collection nil
+ 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
@@ -95,17 +96,18 @@ class SalvageCollectionTest < ActiveSupport::TestCase
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:
@@ -118,7 +120,7 @@ class SalvageCollectionTest < ActiveSupport::TestCase
# 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
+ locator_data = salvage_collection_locator_data BAD_MANIFEST
assert_equal 7, locator_data[0].size
assert_equal false, locator_data[0].include?("foo-faafaafaabd78ad0d6fc3f5b926b450e+foo")
assert_equal true, locator_data[0].include?("faafaafaabd78ad0d6fc3f5b926b450e")
@@ -140,7 +142,7 @@ class SalvageCollectionTest < ActiveSupport::TestCase
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
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