[ARVADOS] updated: 381951637e6688e1868fae9b0642411f5cd1c223

[git at public.curoverse.com]

Summary of changes:
 docker/workbench/application.yml.in               |  3 ++-
 sdk/python/arvados/commands/arv_copy.py           |  5 ++--
 services/api/lib/salvage_collection.rb            |  7 ++++-
 services/api/test/unit/salvage_collection_test.rb | 32 +++++++++++------------
 4 files changed, 27 insertions(+), 20 deletions(-)

       via  381951637e6688e1868fae9b0642411f5cd1c223 (commit)
       via  65f76d01b775c944d2ef6c1673633adb6229d9d8 (commit)
       via  45fcd8aeec29e7e3b86415811f2cf2a5beb82a54 (commit)
       via  d929be450d1886ac04d7c2c98cd16eb44f468413 (commit)
      from  21f6342de550d985db7e2d6964af2ad0f8405406 (commit)

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commit 381951637e6688e1868fae9b0642411f5cd1c223
Author: radhika <radhika at curoverse.com>
Date:   Tue Aug 18 00:29:24 2015 -0400

    6859: mocking Kernel system method had the undersirable side effect of impacting any and all invocations of this method resulting in failures in other tests. Hence, refactored the arv-put invocation into a separate method and mocked this instead in the test. All tests pass now.

diff --git a/services/api/lib/salvage_collection.rb b/services/api/lib/salvage_collection.rb
index 80b96b8..8854cb7 100755
--- a/services/api/lib/salvage_collection.rb
+++ b/services/api/lib/salvage_collection.rb
@@ -15,6 +15,10 @@ module SalvageCollection
   require 'tempfile'
   require 'shellwords'
 
+  def self.salvage_collection_arv_put temp_file
+    %x(arv-put --as-stream --use-filename invalid_manifest_text.txt #{Shellwords::shellescape(temp_file.path)})
+  end
+
   def self.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?
@@ -53,7 +57,8 @@ module SalvageCollection
         temp_file = Tempfile.new('temp')
         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)})
+
+        new_manifest = salvage_collection_arv_put temp_file
 
         temp_file.unlink
 
diff --git a/services/api/test/unit/salvage_collection_test.rb b/services/api/test/unit/salvage_collection_test.rb
index 3efe037..83f3c5b 100644
--- a/services/api/test/unit/salvage_collection_test.rb
+++ b/services/api/test/unit/salvage_collection_test.rb
@@ -4,26 +4,26 @@ require 'salvage_collection'
 TEST_MANIFEST = ". 341dabea2bd78ad0d6fc3f5b926b450e+85626+Ad391622a17f61e4a254eda85d1ca751c4f368da9 at 55e076ce 0:85626:brca2-hg19.fa\n. d7321a918923627c972d8f8080c07d29+82570+A22e0a1d9b9bc85c848379d98bedc64238b0b1532 at 55e076ce 0:82570:brca1-hg19.fa\n"
 
 module Kernel
-  def `(cmd)    # override kernel ` method
-    if cmd.include? 'arv-put'
-      file_contents = file = File.new(cmd.split[-1], "r").gets
-
-      # simulate arv-put error when it is 'user_agreement'
-      if file_contents.include? 'GNU_General_Public_License'
-        return ''
-      else
-        ". " +
-        Digest::MD5.hexdigest(TEST_MANIFEST) +
-        " 0:" + TEST_MANIFEST.length.to_s + ":invalid_manifest_text.txt\n"
-      end
-    end
-  end
-
   def exit code
     raise "Exit code #{code}" if code == 200
   end
 end
 
+module SalvageCollection
+  def self.salvage_collection_arv_put(temp_file)
+    file_contents = file = File.new(temp_file.path, "r").gets
+
+    # simulate arv-put error when it is 'user_agreement'
+    if file_contents.include? 'GNU_General_Public_License'
+      return ''
+    else
+      ". " +
+      Digest::MD5.hexdigest(TEST_MANIFEST) +
+      " 0:" + TEST_MANIFEST.length.to_s + ":invalid_manifest_text.txt\n"
+    end
+  end
+end
+
 class SalvageCollectionTest < ActiveSupport::TestCase
   include SalvageCollection
 
@@ -92,7 +92,7 @@ class SalvageCollectionTest < ActiveSupport::TestCase
     assert_equal true, exited
   end
 
-  test "salvage collection with during arv-put" do
+  test "salvage collection with error during arv-put" do
     # try to salvage collection while mimicking error during arv-put
     status = SalvageCollection.salvage_collection collections('user_agreement').uuid
     assert_equal false, status

commit 65f76d01b775c944d2ef6c1673633adb6229d9d8
Merge: 21f6342 45fcd8a
Author: radhika <radhika at curoverse.com>
Date:   Tue Aug 18 00:06:49 2015 -0400

    Merge branch 'master' into 6859-fix-invalid-manifests


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