require 'tempfile'
require 'shellwords'
- def self.salvage_collection uuid, reason
+ def self.salvage_collection uuid, reason='salvaged - see #6277, #6859'
act_as_system_user do
- if !ENV['ARVADOS_API_TOKEN'] or !ENV['ARVADOS_API_HOST']
- $stderr.puts "Please set ARVADOS_API_HOST and ARVADOS_API_TOKEN environment variables. Exiting."
+ if !ENV['ARVADOS_API_TOKEN'].present? or !ENV['ARVADOS_API_HOST'].present?
+ $stderr.puts "Please set your admin user credentials as ARVADOS environment variables."
exit 1
end
+ if !uuid.present?
+ $stderr.puts "Required uuid argument is missing."
+ return false
+ end
+
src_collection = Collection.find_by_uuid uuid
if !src_collection
$stderr.puts "No collection found for #{uuid}. Returning."
- exit 1
+ return false
end
begin
temp_file.write(src_manifest)
temp_file.close
new_manifest = %x(arv-put --as-stream --use-filename invalid_manifest_text.txt #{Shellwords::shellescape(temp_file.path)})
+
temp_file.unlink
if !new_manifest.present?
$stderr.puts "arv-put --as-stream failed for #{uuid}"
- exit 1
+ return false
end
words = []
puts "Created new collection #{new_collection.uuid}"
rescue => error
$stderr.puts "Error creating collection for #{uuid}: #{error}"
- exit 1
+ return false
end
begin
$stderr.puts "Collection #{uuid} emptied and renamed to #{src_collection.name.inspect}."
rescue => error
$stderr.puts "Error salvaging collection #{new_collection.uuid}: #{error}"
- exit 1
+ return false
end
end
end
--- /dev/null
+require 'test_helper'
+require 'salvage_collection'
+
+TEST_MANIFEST = ". 341dabea2bd78ad0d6fc3f5b926b450e+85626+Ad391622a17f61e4a254eda85d1ca751c4f368da9@55e076ce 0:85626:brca2-hg19.fa\n. d7321a918923627c972d8f8080c07d29+82570+A22e0a1d9b9bc85c848379d98bedc64238b0b1532@55e076ce 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
+
+class SalvageCollectionTest < ActiveSupport::TestCase
+ include SalvageCollection
+
+ setup do
+ set_user_from_auth :admin
+ # arv-put needs ARV env variables
+ ENV['ARVADOS_API_HOST'] = 'unused_by_test'
+ ENV['ARVADOS_API_TOKEN'] = 'unused_by_test'
+ end
+
+ test "salvage test collection" 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'
+
+ # 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 format
+ match = new_collection.manifest_text.match /^. (.*) (.*):invalid_manifest_text.txt\n. (.*) (.*):salvaged_data/
+ assert_not_nil match
+ end
+
+ test "salvage collection with no uuid required argument" do
+ status = SalvageCollection.salvage_collection nil
+ assert_equal false, status
+ end
+
+ test "salvage collection with bogus uuid" do
+ status = SalvageCollection.salvage_collection 'bogus-uuid'
+ assert_equal false, status
+ end
+
+ test "salvage collection with no env ARVADOS_API_HOST" do
+ exited = false
+ begin
+ 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
+ end
+ assert_equal true, exited
+ end
+end