[ARVADOS] updated: a0c7339018d20f9f2c0064c841053f6f1d1a2ccd

Git user git at public.curoverse.com
Wed May 4 16:22:44 EDT 2016


Summary of changes:
 build/run-build-packages-python-and-ruby.sh        |   8 +-
 build/run-build-packages.sh                        |   2 +-
 build/run-tests.sh                                 |  15 +-
 sdk/cli/arvados-cli.gemspec                        |   3 +-
 sdk/cli/bin/arv                                    |   2 +-
 sdk/cli/bin/crunch-job                             |   2 +-
 sdk/cli/test/test_arv-collection-create.rb         |  18 +-
 sdk/cwl/arvados_cwl/__init__.py                    | 150 +++++++++--
 sdk/cwl/setup.py                                   |   2 +-
 sdk/cwl/tests/matcher.py                           |  23 ++
 sdk/cwl/tests/order/empty_order.json               |   1 +
 sdk/cwl/tests/order/inputs_test_order.json         |   9 +
 sdk/cwl/tests/test_job.py                          |  23 +-
 sdk/cwl/tests/test_submit.py                       | 299 +++++++++++++++------
 sdk/cwl/tests/wf/inputs_test.cwl                   |  27 ++
 sdk/python/arvados/commands/put.py                 |  28 +-
 sdk/python/arvados/keep.py                         |  46 +++-
 sdk/python/tests/arvados_testutil.py               |   3 +-
 sdk/python/tests/keepstub.py                       |  14 +
 sdk/python/tests/test_api.py                       |   2 +-
 sdk/python/tests/test_arv_put.py                   |  53 +++-
 sdk/python/tests/test_keep_client.py               | 130 +++++++++
 .../api/app/controllers/application_controller.rb  |   4 +-
 .../v1/api_client_authorizations_controller.rb     |   2 +-
 services/api/config/initializers/fix_www_decode.rb |  16 ++
 services/api/lib/eventbus.rb                       |   2 +-
 services/api/lib/load_param.rb                     |   8 +-
 services/api/lib/record_filters.rb                 |   2 +
 services/api/test/helpers/time_block.rb            |  12 +
 .../integration/collections_performance_test.rb    |  16 +-
 services/api/test/integration/websocket_test.rb    |  36 +--
 services/api/test/test_helper.rb                   |   2 +-
 services/keepstore/azure_blob_volume.go            |  33 ++-
 services/keepstore/azure_blob_volume_test.go       |  18 +-
 services/keepstore/handler_test.go                 |  64 ++++-
 services/keepstore/handlers.go                     |  85 ++++--
 .../keepstore/handlers_with_generic_volume_test.go |  26 +-
 services/keepstore/keepstore.go                    |   1 +
 services/keepstore/keepstore_test.go               |  50 ++--
 services/keepstore/logging_router.go               |  56 ++--
 services/keepstore/logging_router_test.go          |  10 +
 services/keepstore/s3_volume.go                    |  10 +-
 services/keepstore/trash_worker_test.go            |  16 +-
 services/keepstore/volume.go                       |  21 +-
 services/keepstore/volume_generic_test.go          | 168 ++++++------
 services/keepstore/volume_test.go                  |  11 +-
 services/keepstore/volume_unix.go                  |  24 +-
 services/keepstore/volume_unix_test.go             |   8 +-
 .../arvnodeman/computenode/driver/__init__.py      |   6 +-
 .../nodemanager/tests/test_computenode_driver.py   |  61 +++++
 tools/arvbox/lib/arvbox/docker/crunch-setup.sh     |   6 +-
 51 files changed, 1227 insertions(+), 407 deletions(-)
 create mode 100644 sdk/cwl/tests/matcher.py
 create mode 100644 sdk/cwl/tests/order/empty_order.json
 create mode 100644 sdk/cwl/tests/order/inputs_test_order.json
 create mode 100644 sdk/cwl/tests/wf/inputs_test.cwl
 create mode 100644 services/api/config/initializers/fix_www_decode.rb
 create mode 100644 services/keepstore/logging_router_test.go
 create mode 100644 services/nodemanager/tests/test_computenode_driver.py

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commit a0c7339018d20f9f2c0064c841053f6f1d1a2ccd
Merge: 4cd8889 5bd65b0
Author: radhika <radhika at curoverse.com>
Date:   Wed May 4 16:04:49 2016 -0400

    Merge branch 'master' into 8556-trash-untrash-azure-volume
    
    Conflicts:
    	services/keepstore/azure_blob_volume.go
    	services/keepstore/volume_generic_test.go

diff --cc services/keepstore/azure_blob_volume.go
index 444ecfa,9c03743..7c8f8aa
--- a/services/keepstore/azure_blob_volume.go
+++ b/services/keepstore/azure_blob_volume.go
@@@ -152,14 -139,11 +152,14 @@@ func (v *AzureBlobVolume) checkTrashed(
  // If the block is younger than azureWriteRaceInterval and is
  // unexpectedly empty, assume a PutBlob operation is in progress, and
  // wait for it to finish writing.
- func (v *AzureBlobVolume) Get(loc string) ([]byte, error) {
+ func (v *AzureBlobVolume) Get(loc string, buf []byte) (int, error) {
 +	if err := v.checkTrashed(loc); err != nil {
- 		return nil, err
++		return 0, err
 +	}
  	var deadline time.Time
  	haveDeadline := false
- 	buf, err := v.get(loc)
- 	for err == nil && len(buf) == 0 && loc != "d41d8cd98f00b204e9800998ecf8427e" {
+ 	size, err := v.get(loc, buf)
+ 	for err == nil && size == 0 && loc != "d41d8cd98f00b204e9800998ecf8427e" {
  		// Seeing a brand new empty block probably means we're
  		// in a race with CreateBlob, which under the hood
  		// (apparently) does "CreateEmpty" and "CommitData"
diff --cc services/keepstore/volume_generic_test.go
index 35125b8,105795c..0f289ef
--- a/services/keepstore/volume_generic_test.go
+++ b/services/keepstore/volume_generic_test.go
@@@ -455,31 -449,10 +449,32 @@@ func testDeleteOldBlock(t TB, factory T
  	if err := v.Trash(TestHash); err != nil {
  		t.Error(err)
  	}
- 	_, err := v.Get(TestHash)
+ 	data := make([]byte, BlockSize)
 -	if _, err := v.Get(TestHash, data); err == nil || !os.IsNotExist(err) {
++	_, err := v.Get(TestHash, data)
 +	if err == nil || (!os.IsNotExist(err) && !strings.Contains(err.Error(), "Not Found")) {
  		t.Errorf("os.IsNotExist(%v) should have been true", err)
  	}
 +
 +	_, err = v.Mtime(TestHash)
 +	if err == nil || (!os.IsNotExist(err) && !strings.Contains(err.Error(), "Not Found")) {
 +		t.Fatalf("os.IsNotExist(%v) should have been true", err)
 +	}
 +
 +	err = v.Compare(TestHash, TestBlock)
 +	if err == nil || (!os.IsNotExist(err) && !strings.Contains(err.Error(), "Not Found")) {
 +		t.Fatalf("os.IsNotExist(%v) should have been true", err)
 +	}
 +
 +	indexBuf := new(bytes.Buffer)
 +	v.IndexTo("", indexBuf)
 +	if strings.Contains(string(indexBuf.Bytes()), TestHash) {
 +		t.Fatalf("Found trashed block in IndexTo")
 +	}
 +
 +	err = v.Touch(TestHash)
 +	if err == nil || (!os.IsNotExist(err) && !strings.Contains(err.Error(), "Not Found")) {
 +		t.Fatalf("os.IsNotExist(%v) should have been true", err)
 +	}
  }
  
  // Calling Delete() for a block that does not exist should result in error.
@@@ -756,12 -727,12 +749,12 @@@ func testTrashUntrash(t TB, factory Tes
  		}
  	} else if err != nil {
  		if err != ErrNotImplemented {
 -			t.Error(err)
 +			t.Fatal(err)
  		}
  	} else {
- 		_, err = v.Get(TestHash)
+ 		_, err = v.Get(TestHash, buf)
 -		if err == nil || !os.IsNotExist(err) {
 +		if err == nil || (!os.IsNotExist(err) && !strings.Contains(err.Error(), "Not Found")) {
- 			t.Fatalf("os.IsNotExist(%v) should have been true", err)
+ 			t.Errorf("os.IsNotExist(%v) should have been true", err)
  		}
  
  		// Untrash
@@@ -821,28 -791,7 +813,28 @@@ func testTrashEmptyTrashUntrash(t TB, f
  	}
  
  	err = checkGet()
 -	if err == nil || !os.IsNotExist(err) {
 +	if err == nil || (!os.IsNotExist(err) && !strings.Contains(err.Error(), "Not Found")) {
 +		t.Fatalf("os.IsNotExist(%v) should have been true", err)
 +	}
 +
 +	_, err = v.Mtime(TestHash)
 +	if err == nil || (!os.IsNotExist(err) && !strings.Contains(err.Error(), "Not Found")) {
 +		t.Fatalf("os.IsNotExist(%v) should have been true", err)
 +	}
 +
 +	err = v.Compare(TestHash, TestBlock)
 +	if err == nil || (!os.IsNotExist(err) && !strings.Contains(err.Error(), "Not Found")) {
 +		t.Fatalf("os.IsNotExist(%v) should have been true", err)
 +	}
 +
 +	indexBuf := new(bytes.Buffer)
 +	v.IndexTo("", indexBuf)
 +	if strings.Contains(string(indexBuf.Bytes()), TestHash) {
- 		// t.Fatalf("Found trashed block in IndexTo")
++		//t.Fatalf("Found trashed block in IndexTo")
 +	}
 +
 +	err = v.Touch(TestHash)
 +	if err == nil || (!os.IsNotExist(err) && !strings.Contains(err.Error(), "Not Found")) {
  		t.Fatalf("os.IsNotExist(%v) should have been true", err)
  	}
  

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